update

update
New version of GfftoIsoforms

This script is for identifying overlapping CDS sequences in a gff3 file
The input is a gff3 file (-i) and output name without the file extention
(-o)
There is optional input of a non standard 'Name' field (-n)
The output is a txt file showing entries that form overlapping clusters
and a modified gff3 file
Output options are --rename, renameonly and --clusterall
The defult is to create new entries in the gff3 for CDS lines that form
clusters
defult enteries are 'ClusterName','Cluster' and 'ClusterNum'
If --rename is specified then the 'ClusterName' data will instead be
written into 'Name'
--renameonly will do the same as above but also not inclusde the
'Cluster' and 'ClusterNum' enteries
If --clusterall is specified then all CDS lines will be assigned to
clusters (clusters of one)